Contacts of the helix formed by residues 439 - 452 (chain A) in PDB entry 3TVX
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER 439 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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421A ASN* 4.1 4.3 - - - +
437A ASP 3.9 2.4 + - - -
438A GLU* 1.3 72.8 - - - +
440A VAL* 1.3 55.3 + - - +
442A GLU* 3.2 26.7 + - - -
443A ASN* 2.8 39.6 + - - -
481A LEU* 4.2 10.2 + - - +
484A ASP* 3.0 28.5 + - - +
487A LYS* 4.2 17.3 + - - -
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Residues in contact with VAL 440 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421A ASN* 3.4 13.3 + - + +
424A LEU* 4.1 15.0 - - + -
425A ILE* 4.4 9.6 - - + -
431A LEU* 3.6 42.2 - - + +
432A ALA* 3.7 22.4 - - + +
435A TYR* 3.9 8.3 - - + -
437A ASP* 3.8 28.5 - - - +
438A GLU 2.9 7.0 + - - +
439A SER* 1.3 72.9 - - - +
441A LEU* 1.3 58.9 + - - +
443A ASN* 3.3 3.1 + - - +
444A HIS* 2.8 27.4 + - - +
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Residues in contact with LEU 441 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415A ASP 5.1 1.6 - - - +
416A HIS* 3.6 16.6 - - + +
417A PRO* 3.3 29.6 - - + -
419A VAL 3.3 23.8 - - - +
420A SER* 4.0 2.2 - - - -
421A ASN* 2.8 34.9 + - - +
424A LEU* 3.7 16.8 - - + -
431A LEU* 5.2 5.8 - - + -
440A VAL* 1.3 73.1 - - - +
442A GLU* 1.3 59.1 + - - +
444A HIS* 3.0 9.1 + - + +
445A HIS* 2.7 59.5 + - + +
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Residues in contact with GLU 442 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421A ASN* 3.1 27.3 + - - -
439A SER* 3.3 21.8 - - - +
441A LEU* 1.3 82.2 - - - +
443A ASN* 1.3 61.7 + - - +
445A HIS* 3.1 12.3 + - + +
446A LEU* 3.1 28.2 + - - +
480A VAL* 3.8 11.9 - - - +
481A LEU* 4.2 7.2 - - + +
483A THR* 3.8 23.9 - - - +
484A ASP* 3.4 33.9 + - + +
485A MET 4.9 0.2 + - - -
901A MG 4.2 9.9 - - - -
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Residues in contact with ASN 443 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435A TYR* 3.6 34.2 + - + -
438A GLU* 3.1 34.2 + - - +
439A SER* 2.8 27.4 + - - +
440A VAL 3.6 3.8 - - - +
442A GLU* 1.3 74.3 - - - +
444A HIS* 1.3 60.0 + - - +
446A LEU* 3.4 12.1 + - - +
447A ALA* 3.0 23.2 + - - +
481A LEU* 4.1 15.8 - - - +
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Residues in contact with HIS 444 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414A VAL 4.4 2.5 - - - -
415A ASP* 2.7 45.3 + - + -
417A PRO* 6.1 0.2 - - + -
431A LEU* 3.4 45.3 - - + +
435A TYR* 4.0 9.9 + - + -
440A VAL 2.8 14.4 + - - +
441A LEU* 3.0 12.8 + - + +
443A ASN* 1.3 76.5 - - - +
445A HIS* 1.3 61.1 + + - +
447A ALA* 3.4 3.3 + - - +
448A VAL* 3.0 50.0 + - + +
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Residues in contact with HIS 445 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411A ILE* 3.7 15.0 - - - +
412A HIS 3.0 27.6 - - - +
413A ASP* 3.4 26.7 + - - -
414A VAL* 2.6 38.5 + - - +
415A ASP 4.4 0.9 - - - -
416A HIS* 3.7 26.8 - + - -
441A LEU* 2.7 46.1 + - + +
442A GLU* 3.1 13.4 + - + +
444A HIS* 1.3 74.0 - + - +
446A LEU* 1.3 57.7 + - - +
449A GLY* 2.9 26.9 + - - -
480A VAL* 4.3 4.5 - - + -
901A MG 4.1 4.2 - - - -
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Residues in contact with LEU 446 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411A ILE* 4.4 2.9 - - + -
442A GLU 3.1 16.7 + - - +
443A ASN* 3.7 11.7 - - - +
445A HIS* 1.3 75.3 - - - +
447A ALA* 1.3 64.3 + - - +
450A PHE* 3.1 43.7 + - + +
476A VAL* 3.6 24.9 - - + +
477A ILE* 3.8 31.0 - - + +
480A VAL* 3.6 29.2 - - + -
481A LEU* 4.0 25.8 - - + -
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Residues in contact with ALA 447 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435A TYR* 3.5 23.8 - - - +
443A ASN 3.0 9.6 + - - +
444A HIS* 3.7 7.4 - - - +
445A HIS 3.4 0.2 - - - -
446A LEU* 1.3 74.9 - - - +
448A VAL* 1.3 60.6 + - + +
450A PHE* 3.9 2.2 - - - +
451A LYS* 2.9 33.9 + - - +
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Residues in contact with VAL 448 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364A HIS* 4.7 6.3 - - + -
414A VAL* 3.9 29.8 - - + -
415A ASP* 4.2 11.9 - - + +
444A HIS* 3.0 51.5 + - + +
447A ALA* 1.3 73.8 - - + +
449A GLY* 1.3 66.7 + - - +
451A LYS* 3.3 24.9 + - - +
452A LEU* 3.1 41.7 + - + +
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Residues in contact with GLY 449 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357A TYR* 2.7 32.6 + - - -
361A LEU* 4.7 4.0 - - - -
407A PHE* 4.1 6.0 - - - -
411A ILE* 4.1 18.6 - - - -
414A VAL* 3.9 4.6 - - - +
445A HIS 2.9 17.8 + - - -
446A LEU 4.0 0.7 - - - -
448A VAL* 1.3 78.2 - - - +
450A PHE* 1.3 60.3 + - - +
452A LEU* 3.7 4.7 + - - +
453A LEU* 4.1 0.5 + - - +
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Residues in contact with PHE 450 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407A PHE* 3.9 16.2 - + - -
411A ILE* 4.6 2.0 - - + -
446A LEU* 3.1 40.1 + - + +
447A ALA* 4.2 2.2 - - - +
449A GLY* 1.3 72.6 - - - +
451A LYS* 1.3 65.0 + - - +
452A LEU 3.1 2.2 - - - -
453A LEU* 3.2 41.2 + - + +
454A GLN* 4.4 6.6 + - - +
461A PHE* 4.8 2.0 - + - -
472A LEU* 4.4 10.5 - - + -
473A ARG* 4.0 34.5 - - + -
476A VAL* 3.7 38.6 - - + -
477A ILE* 5.0 2.9 - - + -
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Residues in contact with LYS 451 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364A HIS* 4.6 12.1 + - - -
447A ALA 2.9 17.8 + - - +
448A VAL* 3.4 31.6 - - - +
450A PHE* 1.3 76.7 - - - +
452A LEU* 1.3 82.4 + - + +
454A GLN* 3.2 32.1 + - - +
455A GLU* 4.1 8.5 + - - +
430B GLU* 3.3 44.1 + - + +
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Residues in contact with LEU 452 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357A TYR* 3.8 17.4 - - + -
360A THR* 3.9 7.0 - - + -
361A LEU* 4.0 31.2 - - + -
364A HIS* 3.9 43.3 - - + +
448A VAL* 3.1 30.5 + - + +
449A GLY 3.9 0.7 - - - +
450A PHE 3.1 1.0 - - - -
451A LYS* 1.3 88.6 - - - +
453A LEU* 1.3 60.6 + - - +
454A GLN 3.0 6.5 + - - -
455A GLU* 3.1 42.1 + - - +
458A CYS* 3.1 14.2 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il